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Issue #4: Update _establish_structure_mappping to not fail when serial number 0 is present #5

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Issue #4: Update _establish_structure_mappping to not fail when serial number 0 is present #5

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24 changes: 17 additions & 7 deletions arpeggio/core/interactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1987,18 +1987,28 @@ def _establish_structure_mappping(self):
# FIRST MAP PDB SERIAL NUMBERS TO BIOPYTHON ATOMS FOR SPEED LATER
# THIS AVOIDS LOOPING THROUGH `s_atoms` MANY TIMES
serial_to_bio = {x.serial_number: x for x in self.s_atoms}
for ob_atom in ob.OBMolAtomIter(self.ob_mol):
serial = ob_atom.GetId()

# `Id` IS A UNIQUE AND STABLE ID IN OPENBABEL
# CAN RECOVER THE ATOM WITH `mol.GetAtomById(id)`
serial_to_ob = {x.GetId(): x for x in ob.OBMolAtomIter(self.ob_mol)}

if 0 in serial_to_ob and 0 not in serial_to_bio:
offset = 1
logging.debug('OB atom serial numbers start with 0, but there are no BioPython atoms with serial number 0. Adding 1 to all OB serials for mapping purposes.')
else:
offset = 0

for serial, ob_atom in serial_to_ob.items():
# MATCH TO THE BIOPYTHON ATOM BY SERIAL NUMBER
try:
biopython_atom = serial_to_bio[serial]

biopython_atom = serial_to_bio[serial + offset]
except KeyError:
raise OBBioMatchError(serial)
raise OBBioMatchError("Failed to match OB atom to a BioPython atom: {},{} : {}({})".format(serial, serial + offset, ob_atom.GetType()[:1], ob_atom.GetType()))

# Sanity check that elements match, for debugging
if ob_atom.GetType()[:1] != biopython_atom.element[:1]:
raise OBBioMatchError("Failed to correctly match atoms with different elements: {},{} : {}({}) != {}({}, {})".format(serial, serial + offset, ob_atom.GetType()[:1], ob_atom.GetType(), biopython_atom.element[:1], biopython_atom.element, biopython_atom.name))

# `Id` IS A UNIQUE AND STABLE ID IN OPENBABEL
# CAN RECOVER THE ATOM WITH `mol.GetAtomById(id)`
self.ob_to_bio[ob_atom.GetId()] = biopython_atom
self.bio_to_ob[biopython_atom] = ob_atom.GetId()

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